comparison abims_xcms_xcmsSet.xml @ 29:5dba1c94fb94 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

28:b90e4f92e8b5

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>

    <macros>
        <import>macros.xml</import>
    </macros>

        xfunction xcmsSet

        xsetRdataOutput '$xsetRData'
        sampleMetadataOutput '$sampleMetadata'
        ticspdf '$ticsRawPdf'
        bicspdf '$bpcsRawPdf'


        #if $options_scanrange.option == "show":
            scanrange "c($options_scanrange.scanrange)"
        #end if

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if
        @COMMAND_LOG_EXIT@
    ]]></command>

    <inputs>

        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

                <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
                <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
                <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
        <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
        </data>
        <data name="ticsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
    </outputs>

    <tests>
        <!--<test>
            <param name="input" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />
            <param name="methods|step" value="0.01" />
            <param name="methods|fwhm" value="4" />
            <param name="methods|options_m|option" value="show" />
            <param name="methods|options_m|max" value="50" />
            <param name="methods|options_m|snthresh" value="1" />
            <param name="methods|options_m|steps" value="2" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="sacuri_current_root.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />

                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
        <!-- Passed but disable to save time for Travis" -->
        <!--<test>
            <param name="input" value="ko15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 1 samples" />
                    <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
                    <has_text text="Mass range: 200.2-600 m/z" />
                    <has_text text="Peaks: 2262 (about 2262 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="ko16.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 1 samples" />
                    <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 2408 (about 2408 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="wt15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>
                    <has_text text="object with 1 samples" />
                    <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
                    <has_text text="Mass range: 200.2-599.8 m/z" />
                    <has_text text="Peaks: 2278 (about 2278 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="wt16.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />

                    <has_text text="Peaks: 380 (about 380 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="MM14.mzML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="56" />

                    <has_text text="Peaks: 222 (about 222 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[

============
Xcms.xcmsSet
============

-----------
Description
-----------

This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
You can read a tutorial on how to perform xcms preprocessing which is available here_.

.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf


-----------------
Workflow position
-----------------

**Upstream tools**

========================= ================= ======= =========
Name                      output file       format  parameter
========================= ================= ======= =========
NA                        NA                zip     NA
========================= ================= ======= =========


**Downstream tools**

+---------------------------+--------------------+-----------------+
| Name                      | Output file        | Format          |
+===========================+====================+=================+
|xcms.group                 | xset.RData         | rdata.xcms.raw  |
+---------------------------+--------------------+-----------------+
|PCA ellipsoid by factors   | sampleMetadata.tsv | Tabular         |
+---------------------------+--------------------+-----------------+
|Anova                      | sampleMetadata.tsv | Tabular         |
+---------------------------+--------------------+-----------------+


**Example of a metabolomic workflow**

.. image:: xcms_xcmsset_workflow.png


------

.. class:: infomark

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

---------------------------------------------------



-----------
Input files
-----------

+---------------------------+----------------------------------+
| Parameter : num + label   |   Format                         |
+===========================+==================================+
| OR : Zip file             |   zip                            |
+---------------------------+----------------------------------+
| OR : Single file          |   mzXML, mzML, mzData, netCDF    |
+---------------------------+----------------------------------+

**Choose your inputs**

You have two methods for your inputs:

    | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
    | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).

Zip file: Steps for creating the zip file
-----------------------------------------

**Step1: Creating your directory and hierarchize the subdirectories**


VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).

Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
arabidopsis/wild/01.raw
arabidopsis/mutant/01.raw

**Step2: Creating a zip file**

Create your zip file (e.g.: arabidopsis.zip).

**Step 3 : Uploading it to our Galaxy server**

If your zip file is less than 2Gb, you get use the Get Data tool to upload it.

Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).

For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).

Advices for converting your files for the XCMS input
----------------------------------------------------

We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.

**We recommend you the following parameters:**

Use Filtering: **True**

Use Peak Picking: **True**

Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode

Use zlib: **64**

Binary Encoding: **64**

m/z Encoding: **64**

Intensity Encoding: **64**


----------
Parameters
----------

------------
Output files
------------

xset.TICs_raw.pdf

    | "Total Ion Chromatograms" graph in pdf format.

xset.BPCs_raw.pdf

    | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.

sampleMetadata.tsv

    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
    | This file is necessary in the Anova and PCA step of the workflow.

xset.RData: rdata.xcms.raw format

    | Rdata file that is necessary in the second step of the workflow "xcms.group".

------

.. class:: infomark

The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.

---------------------------------------------------

---------------
Working example
---------------

Input files
-----------

    | zip_file -> **sacuri.zip**

Parameters
----------

    | Method -> **matchedFilter**
    | step   -> **0.01**
    | fwhm   -> **4**
    | Advanced option -> **show**
    | max: -> **50**
    | snthresh -> **1**
    | steps -> **2**


Output files
------------

    | **1) xset.RData: RData file**

    | **2) Example of a sampleMetadata.tsv  :**


+---------------------------+------------+---------+
| sampleMetadata            |   class    | polarity|
+===========================+============+=========+
|HU_neg_017                 |   bio      |negative |
+---------------------------+------------+---------+
|HU_neg_028                 |   bio      |negative |
+---------------------------+------------+---------+
|HU_neg_034                 |   bio      |negative |
+---------------------------+------------+---------+
|Blanc04                    |   blank    |negative |
+---------------------------+------------+---------+
|Blanc06                    |   blank    |negative |
+---------------------------+------------+---------+
|Blanc09                    |   blank    |negative |
+---------------------------+------------+---------+



    | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**

.. image:: xcms_tics.png


---------------------------------------------------

Changelog/News
--------------

**Version 2.1.0 - 22/02/2017**

- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".

- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1

- UPDATE: refactoring of internal management of inputs/outputs

- TEST: refactoring to feed the new report tool


**Version 2.0.2 - 18/01/2016

- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.


**Version 2.0.2 - 09/10/2015**

29:5dba1c94fb94

<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0">
    <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>

    <macros>
        <import>macros.xml</import>
    </macros>

        xfunction xcmsSet

        xsetRdataOutput '$xsetRData'
        sampleMetadataOutput '$sampleMetadata'

        #if $options_scanrange.option == "show":
            scanrange "c($options_scanrange.scanrange)"
        #end if

            winSize.noise $methods.winSize_noise
            amp.Th $methods.amp_Th
            scales "c($methods.scales)"
            SNR.method "$methods.SNR_method"
        #end if

        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
            && mv *-TIC_mqc.out $ticsRawTab
            && mv *-BPC_mqc.out $bpcsRawTab
        #end if

        @COMMAND_LOG_EXIT@;
    ]]></command>

    <inputs>

        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />

                <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
                <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
                <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
            </when>
        </conditional>


        <expand macro="input_tic_bpc_pdf"/>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />

        <!-- SINGLE MODE -->
        <data name="ticsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.tabular">
            <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
        </data>
        <data name="bpcsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.tabular">
            <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
        </data>

        <!-- ZIP MODE -->
        <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
        </data>
        <data name="ticsRawPdf" format="pdf" from_work_dir="TICs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
            <filter>tic_bpc_pdf</filter>
        </data>
        <data name="bpcsRawPdf" format="pdf" from_work_dir="BPCs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
            <filter>tic_bpc_pdf</filter>
        </data>
        <collection name="ticsRawTabCollection" type="list" label="TIC raw tabular">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)-TIC_mqc\.out" ext="tabular" visible="true" />
        </collection>
        <collection name="bpcsRawTabCollection" type="list" label="BPC raw tabular">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)-BPC_mqc\.out" ext="tabular" visible="true" />
        </collection>
    </outputs>

    <tests>
        <!--
        <test>
            <param name="input" value="sacuri_current_root.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />

                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
            <output_collection name="ticsRawTabCollection" type="list">
                <element name="ko15" value="ko15-TIC_mqc.out" />
                <element name="ko16" value="ko16-TIC_mqc.out" />
                <element name="wt15" value="wt15-TIC_mqc.out" />
                <element name="wt16" value="wt16-TIC_mqc.out" />
            </output_collection>
            <output_collection name="bpcsRawTabCollection" type="list">
                <element name="ko15" value="ko15-BPC_mqc.out" />
                <element name="ko16" value="ko16-BPC_mqc.out" />
                <element name="wt15" value="wt15-BPC_mqc.out" />
                <element name="wt16" value="wt16-BPC_mqc.out" />
            </output_collection>
        </test>
        <!-- Passed but disable to save time for Travis" -->
        <!--
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="wt16.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />

                    <has_text text="Peaks: 380 (about 380 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
            <output name="ticsRawTab" value="HU_neg_017-TIC_mqc.out" />
            <output name="bpcsRawTab" value="HU_neg_017-BPC_mqc.out" />
        </test>
        <test>
            <param name="input" value="MM14.mzML"  ftype="mzxml" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="56" />

                    <has_text text="Peaks: 222 (about 222 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
            <output name="ticsRawTab" value="MM14-TIC_mqc.out" />
            <output name="bpcsRawTab" value="MM14-BPC_mqc.out" />
        </test>
    </tests>

    <help><![CDATA[

============
Xcms.xcmsSet
============

Description
-----------

This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
You can read a tutorial on how to perform xcms preprocessing which is available here_.

.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf


Workflow position
-----------------

**Upstream tools**

+------------------------+--------------------+-----------------------------+-----------+
| Name                   | output file        | format                      | parameter |
+------------------------+--------------------+-----------------------------+-----------+
| Upload File            | Dataset Collection | mzXML, mzML, mzData, netCDF | NA        |
+------------------------+--------------------+-----------------------------+-----------+

**Downstream tools**

+---------------------------+--------------------+-----------------+
| Name                      | Output file        | Format          |
+===========================+====================+=================+
|xcms.group                 | xset.RData         | rdata.xcms.raw  |
+---------------------------+--------------------+-----------------+


**Example of a metabolomic workflow**

.. image:: xcms_xcmsset_workflow.png

---------------------------------------------------

-----------
Input files
-----------

Choose your inputs
------------------

+---------------------------+----------------------------------+
| Parameter                 |   Format                         |
+===========================+==================================+
| OR : Single file          |   mzXML, mzML, mzData, netCDF    |
+---------------------------+----------------------------------+
| OR : Zip file             |   zip                            |
+---------------------------+----------------------------------+

You have two methods for your inputs:

* Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"

* Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).

Single file
-----------

This method is recommended because:

* Since files are uploaded indivudially, they are smaller. And so they should be able to be uploaded using the Get Data tools.

* It allow you to launch your xcmsSet in parallele.

You just have to create a Dataset Collection as explain in this video_

.. _video: http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v


Zip file
--------

This method isn't recommended because zip file aren't really well integrated

Steps for creating the zip file

**Step1: Creating your directory and hierarchize the subdirectories**


    | **VERY IMPORTANT**: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
    | Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
    | - arabidopsis/wild/01.raw
    | - arabidopsis/mutant/01.raw

**Step2: Creating a zip file**

    | Create your zip file (e.g.: arabidopsis.zip).

**Step 3 : Uploading it to our Galaxy server**

    | If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
    | Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
    | For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
    | Advices for converting your files for the XCMS input

Raw file format
---------------

We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xcms centWave method.

**We recommend you the following parameters:**

    | **Use Filtering**: True
    | **Use Peak Picking**: True
    | **Peak Peaking**: -Apply to MS Levels: All Levels (1-) : Centroid Mode
    | **Use zlib**: 64
    | **Binary Encoding**: 64
    | **m/z Encoding**: 64
    | **Intensity Encoding**: 64


----------
Parameters
----------

------------
Output files
------------

xset.RData: rdata.xcms.raw format

    | Rdata file that is necessary in the second step of the workflow "xcms.group".

@HELP_BCP_TIC@

sampleMetadata.tsv [if using zip]

    | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
    | This file is necessary in the Batch correction and statictics steps of the workflow.

---------------------------------------------------

---------------
Working example
---------------

Input files
-----------

    | Dataset Collection -> build using this dataset_

.. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip

Parameters
----------

    | **Method**: centWave
    | **Max tolerated ppm m/z deviation in consecutive scans in ppm**: 25
    | **Min,Max peak width in seconds**: 10,40
    | **Advanced option**: show
    | **Signal/Noise threshold**: 50
    | **Minimum difference in m/z for peaks with overlapping retention times**: 1
    | **Prefilter step for the first phase**: 3,100


---------------------------------------------------

Changelog/News
--------------

**Version 2.2.0 - 19/10/2017**

- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.

**Version 2.1.0 - 22/02/2017**

- NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".

- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1

- UPDATE: refactoring of internal management of inputs/outputs

- TEST: refactoring to feed the new report tool


**Version 2.0.2 - 18/01/2016**

- BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.


**Version 2.0.2 - 09/10/2015**